If you're happy with the version of LW you have, then maybe stick with it until 4.1 comes out. Other than what murasame suggested, I could only suggest to go 'utility' correction be that mac or 3rd party such as the usual main ones (Norton, Diskwarrior, TechTool Pro.) Startup from the Panther startup disk & repair permissions & check the other mac utilities. Previously in OS9 when you installed/updated software there could be minor problems which could be repaired by rebuilding the desktop or/& using 3rd utilities to adjust everything to normal. But OSX is not so obvious. Try my earlier suggestions & see if it makes a difference. If not, (& please try both mac & 3rd party) then repost back her to this thread.

By the way, DiskWarrior not only rebuilds the desktop but repairs any damage to the directory info. which is vital info. Otherwise you'll have saving issues, etc.